nextflow.scm

The nextflow.scm package defines the Git provider interface and implements several built-in Git providers. It also manages local pipeline repositories using a Strategy pattern to support different repository management approaches.

Class Diagram

classDiagram %% %% nextflow.scm %% direction LR CmdRun --> AssetManager : run class AssetManager { project : String mainScript : String provider : RepositoryProvider strategy : RepositoryStrategy hub : String providerConfigs : List~ProviderConfig~ } class RepositoryStrategyType { <<enumeration>> LEGACY MULTI_REVISION } AssetManager --> RepositoryStrategyType AssetManager "1" --o "1" RepositoryStrategy AssetManager "1" --o "1" RepositoryProvider AssetManager "1" --* "*" ProviderConfig class RepositoryStrategy { <<interface>> } class AbstractRepositoryStrategy { <<abstract>> project : String provider : RepositoryProvider root : File } class LegacyRepositoryStrategy { localPath : File } class MultiRevisionRepositoryStrategy { revision : String bareRepo : File commitPath : File revisionSubdir : File } RepositoryStrategy <|-- AbstractRepositoryStrategy AbstractRepositoryStrategy <|-- LegacyRepositoryStrategy AbstractRepositoryStrategy <|-- MultiRevisionRepositoryStrategy class RepositoryProvider { <<abstract>> } RepositoryStrategy --> RepositoryProvider RepositoryProvider <|-- AzureRepositoryProvider RepositoryProvider <|-- BitbucketRepositoryProvider RepositoryProvider <|-- BitbucketServerRepositoryProvider RepositoryProvider <|-- GiteaRepositoryProvider RepositoryProvider <|-- GithubRepositoryProvider RepositoryProvider <|-- GitlabRepositoryProvider RepositoryProvider <|-- LocalRepositoryProvider

Note

Some classes may be excluded from the above diagram for brevity.

Architecture overview

Repository strategies

The AssetManager uses the Strategy pattern to support different ways of managing local pipeline installations:

• LegacyRepositoryStrategy: Traditional approach where each project gets a full git clone in $NXF_HOME/{project} directory. Only one revision can exist at a time per project.

• MultiRevisionRepositoryStrategy: Modern approach that allows multiple revisions to coexist efficiently by:

  • Maintaining a shared bare repository in $NXF_HOME/.repos/{project}/bare/

  • Creating lightweight clones for each commit in $NXF_HOME/.repos/{project}/clones/{commitId}/

  • Sharing git objects between revisions to minimize disk space

Strategy selection

The AssetManager automatically selects the appropriate strategy based on:

1. Environment variable: NXF_SCM_LEGACY=true forces legacy mode

2. Repository status: Detected by checking existing repository structure:

   • UNINITIALIZED: No repository exists, use Multi-Revision (default)

   • LEGACY_ONLY: Only legacy .git directory exists, use Legacy

   • BARE_ONLY: Only bare repository exists, use Multi-Revision

   • HYBRID: Both exist, prefer Multi-Revision

Repository provider

The RepositoryProvider class is the base class for all Git providers. It defines how to authenticate with the provider, clone a Git repository, inspect branches and tags, etc. The provider is used by repository strategies to interact with remote Git services.

Key components

AssetManager

Central class that manages pipeline assets. Key responsibilities include:

• Project name resolution and validation

• Strategy selection and initialization

• Provider configuration and authentication

• Repository download and checkout operations

• Coordination between strategy and provider

RepositoryStrategy

Interface defining for repository management operations:

• download(): Download or update a revision

• checkout(): Switch to a specific revision

• drop(): Delete local copies

• getLocalPath(): Get path to working directory

• getGit(): Access JGit repository instance